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Genome-wide association study

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https://www.readbyqxmd.com/read/28335576/genome-wide-identification-and-evolutionary-analysis-of-sarcocystis-neurona-protein-kinases
#1
Edwin K Murungi, Henry M Kariithi
The apicomplexan parasite Sarcocystis neurona causes equine protozoal myeloencephalitis (EPM), a degenerative neurological disease of horses. Due to its host range expansion, S. neurona is an emerging threat that requires close monitoring. In apicomplexans, protein kinases (PKs) have been implicated in a myriad of critical functions, such as host cell invasion, cell cycle progression and host immune response evasion. Here, we used various bioinformatics methods to define the kinome of S. neurona and phylogenetic relatedness of its PKs to other apicomplexans...
March 21, 2017: Pathogens
https://www.readbyqxmd.com/read/28335481/genetic-variants-contributing-to-colistin-cytotoxicity-identification-of-tgif1-and-hoxd10-using-a-population-genomics-approach
#2
Michael T Eadon, Ronald J Hause, Amy L Stark, Ying-Hua Cheng, Heather E Wheeler, Kimberly S Burgess, Eric A Benson, Patrick N Cunningham, Robert L Bacallao, Pierre C Dagher, Todd C Skaar, M Eileen Dolan
Colistin sulfate (polymixin E) is an antibiotic prescribed with increasing frequency for severe Gram-negative bacterial infections. As nephrotoxicity is a common side effect, the discovery of pharmacogenomic markers associated with toxicity would benefit the utility of this drug. Our objective was to identify genetic markers of colistin cytotoxicity that were also associated with expression of key proteins using an unbiased, whole genome approach and further evaluate the functional significance in renal cell lines...
March 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335076/fine-mapping-of-chromosome-5p15-33-identifies-novel-lung-cancer-susceptibility-loci-in-han-chinese
#3
Jing Dong, Yang Cheng, Meng Zhu, Yang Wen, Cheng Wang, Yuzhuo Wang, Liguo Geng, Wei Shen, Jia Liu, Zhihua Li, Jiahui Zhang, Hongxia Ma, Juncheng Dai, Guangfu Jin, Zhibin Hu, Hongbing Shen
Genome-wide association studies in European and Asian populations have consistently identified chromosome 5p15.33 as a lung cancer susceptibility region. To investigate further the genetic architecture of common variants in this region, we conducted a two-stage fine-mapping analysis discovered by targeted resequencing of 200 cases and 300 controls individually, and validated in multiethnic lung cancer GWASs with 12,843 cases and 12,639 controls. Two independent variants were identified in approximate conditional analysis with GCTA and consistently validated in lung cancer GWASs in both Asian and European populations...
March 23, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28335028/defining-the-5%C3%AE-and-3%C3%AE-landscape-of-the-drosophila-transcriptome-with-exo-seq-and-rnaseh-seq
#4
Shaked Afik, Osnat Bartok, Maxim N Artyomov, Alexander A Shishkin, Sabah Kadri, Mor Hanan, Xiaopeng Zhu, Manuel Garber, Sebastian Kadener
Cells regulate biological responses in part through changes in transcription start sites (TSS) or cleavage and polyadenylation sites (PAS). To fully understand gene regulatory networks, it is therefore critical to accurately annotate cell type-specific TSS and PAS. Here we present a simple and straightforward approach for genome-wide annotation of 5΄- and 3΄-RNA ends. Our approach reliably discerns bona fide PAS from false PAS that arise due to internal poly(A) tracts, a common problem with current PAS annotation methods...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28335003/identification-of-genetic-variants-affecting-vitamin-d-receptor-binding-and-associations-with-autoimmune-disease
#5
Giuseppe Gallone, Wilfried Haerty, Giulio Disanto, Sreeram V Ramagopalan, Chris P Ponting, Antonio J Berlanga-Taylor
Large numbers of statistically significant associations between sentinel SNPs and case-control status have been replicated by genome-wide association studies. Nevertheless, few underlying molecular mechanisms of complex disease are currently known. We investigated whether variation in binding of a transcription factor, the vitamin D receptor (VDR) whose activating ligand vitamin D has been proposed as a modifiable factor in multiple disorders, could explain any of these associations. VDR modifies gene expression by binding DNA as a heterodimer with the Retinoid X receptor (RXR)...
March 9, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334977/sclip-an-integrated-platform-to-study-rna-protein-interactomes-in-biomedical-research-identification-of-cstf2tau-in-alternative-processing-of-small-nuclear-rnas
#6
Yulia Kargapolova, Michal Levin, Karl Lackner, Sven Danckwardt
RNA-binding proteins (RBPs) are central for gene expression by controlling the RNA fate from birth to decay. Various disorders arising from perturbations of RNA-protein interactions document their critical function. However, deciphering their function is complex, limiting the general functional elucidation of this growing class of proteins and their contribution to (patho)physiology. Here, we present sCLIP, a simplified and robust platform for genome-wide interrogation of RNA-protein interactomes based on crosslinking-immunoprecipitation and high-throughput sequencing...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334972/enrichment-methods-provide-a-feasible-approach-to-comprehensive-and-adequately-powered-investigations-of-the-brain-methylome
#7
Robin F Chan, Andrey A Shabalin, Lin Y Xie, Daniel E Adkins, Min Zhao, Gustavo Turecki, Shaunna L Clark, Karolina A Aberg, Edwin J C G van den Oord
Methylome-wide association studies are typically performed using microarray technologies that only assay a very small fraction of the CG methylome and entirely miss two forms of methylation that are common in brain and likely of particular relevance for neuroscience and psychiatric disorders. The alternative is to use whole genome bisulfite (WGB) sequencing but this approach is not yet practically feasible with sample sizes required for adequate statistical power. We argue for revisiting methylation enrichment methods that, provided optimal protocols are used, enable comprehensive, adequately powered and cost-effective genome-wide investigations of the brain methylome...
February 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334950/downstream-targets-of-gwas-detected-genes-for-breast-lung-and-prostate-and-colon-cancer-converge-to-g1-s-transition-pathway
#8
Olga Y Gorlova, Eugene I Demidenko, Christopher I Amos, Ivan P Gorlov
Genome-wide association studies (GWASs) identified over 500 single nucleotide polymorphisms (SNPs) influencing cancer risk. It is logical to expect the cancer-associated genes to cluster in pathways directly involved in carcinogenesis, e.g. cell cycle. Nevertheless, analyses of the GWAS-detected cancer risk genes usually show no or weak enrichment by known cancer genes.We hypothesized that GWAS-detected cancer risk-associated genes function as upstream regulators of the genes directly involved in carcinogenesis...
March 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334935/genome-wide-association-study-of-iron-traits-and-relation-to-diabetes-in-the-hispanic-community-health-study-study-of-latinos-hchs-sol-potential-genomic-intersection-of-iron-and-glucose-regulation
#9
Laura M Raffield, Tin Louie, Tamar Sofer, Deepti Jain, Eli Ipp, Kent D Taylor, George J Papanicolaou, Larissa Avilés-Santa, Leslie A Lange, Cathy C Laurie, Matthew P Conomos, Timothy A Thornton, Yii-Der Ida Chen, Qibin Qi, Scott Cotler, Bharat Thyagarajan, Neil Schneiderman, Jerome I Rotter, Alex P Reiner, Henry J Lin
Genetic variants contribute to normal variation of iron-related traits and may also cause clinical syndromes of iron deficiency or excess. Iron overload and deficiency can adversely affect human health. For example, elevated iron storage is associated with increased diabetes risk, although mechanisms are still being investigated. We conducted the first genome-wide association study (GWAS) of serum iron, total iron binding capacity (TIBC), transferrin saturation, and ferritin in a Hispanic/Latino cohort, the Hispanic Community Health Study/Study of Latinos (HCHS/SOL; >12,000 participants) and also assessed the generalization of previously known loci to this population...
March 7, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334899/association-analyses-of-east-asian-individuals-and-trans-ancestry-analyses-with-european-individuals-reveal-new-loci-associated-with-cholesterol-and-triglyceride-levels
#10
Cassandra N Spracklen, Peng Chen, Young Jin Kim, Xu Wang, Hui Cai, Shengxu Li, Jirong Long, Ying Wu, Ya Xing Wang, Fumihiko Takeuchi, Jer-Yuarn Wu, Keum-Ji Jung, Cheng Hu, Koichi Akiyama, Yonghong Zhang, Sanghoon Moon, Todd A Johnson, Huaixing Li, Rajkumar Dorajoo, Meian He, Maren E Cannon, Tamara S Roman, Elias Salfati, Keng-Hung Lin, Xiuqing Guo, Wayne H H Sheu, Devin Absher, Linda S Adair, Themistocles L Assimes, Tin Aung, Qiuyin Cai, Li-Ching Chang, Chien-Hsiun Chen, Li-Hsin Chien, Lee-Ming Chuang, Shu-Chun Chuang, Shufa Du, Qiao Fan, Cathy S J Fann, Alan B Feranil, Yechiel Friedlander, Penny Gordon-Larsen, Dongfeng Gu, Lixuan Gui, Zhirong Guo, Chew-Kiat Heng, James Hixson, Xuhong Hou, Chao Agnes Hsiung, Yao Hu, Mi Yeong Hwang, Chii-Min Hwu, Masato Isono, Jyh-Ming Jimmy Juang, Chiea-Chuen Khor, Yun Kyoung Kim, Woon-Puay Koh, Michiaki Kubo, I-Te Lee, Sun-Ju Lee, Wen-Jane Lee, Kae-Woei Liang, Blanche Lim, Sing-Hui Lim, Jianjun Liu, Toru Nabika, Wen-Harn Pan, Hao Peng, Thomas Quertermous, Charumathi Sabanayagam, Kevin Sandow, Jinxiu Shi, Liang Sun, Pok Chien Tan, Shu-Pei Tan, Kent D Taylor, Yik-Ying Teo, Sue-Anne Toh, Tatsuhiko Tsunoda, Rob M van Dam, Aili Wang, Feijie Wang, Jie Wang, Wen Bin Wei, Yong-Bing Xiang, Jie Yao, Jian-Min Yuan, Rong Zhang, Wanting Zhao, Yii-Der Ida Chen, Stephen S Rich, Jerome I Rotter, Tzung-Dau Wang, Tangchun Wu, Xu Lin, Bok-Ghee Han, Toshihiro Tanaka, Yoon Shin Cho, Tomohiro Katsuya, Weiping Jia, Sun-Ha Jee, Yuan-Tsong Chen, Norihiro Kato, Jost B Jonas, Ching-Yu Cheng, Xiao-Ou Shu, Jiang He, Wei Zheng, Tien-Yin Wong, Wei Huang, Bong-Jo Kim, E-Shyong Tai, Karen L Mohlke, Xueling Sim
Large-scale meta-analyses of genome-wide association studies (GWAS) have identified >175 loci associated with fasting cholesterol levels, including total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG). With differences in linkage disequilibrium (LD) structure and allele frequencies between ancestry groups, studies in additional large samples may detect new associations. We conducted staged GWAS meta-analyses in up to 69,414 East Asian individuals from 24 studies with participants from Japan, the Philippines, Korea, China, Singapore, and Taiwan...
February 21, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334860/genetic-regulation-of-gene-expression-in-the-epileptic-human-hippocampus
#11
Nasir Mirza, Richard Appleton, Sasha Burn, Daniel du Plessis, Roderick Duncan, Jibril Osman Farah, Bjarke Feenstra, Anders Hviid, Vivek Josan, Rajiv Mohanraj, Arif Shukralla, Graeme J Sills, Anthony G Marson, Munir Pirmohamed
Epilepsy is a serious and common neurological disorder. Expression quantitative loci (eQTL) analysis is a vital aid for the identification and interpretation of disease-risk loci. Many eQTLs operate in a tissue- and condition-specific manner. We have performed the first genome-wide cis-eQTL analysis of human hippocampal tissue to include not only normal (n = 22) but also epileptic (n = 22) samples. We demonstrate that disease-associated variants from an epilepsy GWAS meta-analysis and a febrile seizures (FS) GWAS are significantly more enriched with epilepsy-eQTLs than with normal hippocampal eQTLs from two larger independent published studies...
March 3, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334818/chromosomal-dynamics-predicted-by-an-elastic-network-model-explains-genome-wide-accessibility-and-long-range-couplings
#12
Natalie Sauerwald, She Zhang, Carl Kingsford, Ivet Bahar
Understanding the three-dimensional (3D) architecture of chromatin and its relation to gene expression and regulation is fundamental to understanding how the genome functions. Advances in Hi-C technology now permit us to study 3D genome organization, but we still lack an understanding of the structural dynamics of chromosomes. The dynamic couplings between regions separated by large genomic distances (>50 Mb) have yet to be characterized. We adapted a well-established protein-modeling framework, the Gaussian Network Model (GNM), to model chromatin dynamics using Hi-C data...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334814/genome-wide-association-study-identifies-novel-susceptible-loci-and-highlights-wnt-beta-catenin-pathway-in-the-development-of-adolescent-idiopathic-scoliosis
#13
Zezhang Zhu, Leilei Xu, Nelson Leung-Sang Tang, Xiaodong Qin, Zhenhua Feng, Weixiang Sun, Weiguo Zhu, Benlong Shi, Peng Liu, Saihu Mao, Jun Qiao, Zhen Liu, Xu Sun, Fangcai Li, Jack Chun-Yiu Cheng, Yong Qiu
The genetic architecture of adolescent idiopathic scoliosis (AIS) remains poorly understood. Here we present the result of a 4-stage genome-wide association study composed of 5,953 AIS patients and 8,137 controls. Overall, we identified three novel susceptible loci including rs7593846 at 2p14 near MEIS1 (Pcombined = 1.19 × 10-13, OR = 1.21, 95% CI = 1.10-1.32), rs7633294 at 3p14.1 near MAGI1 (Pcombined = 1.85 × 10-12, OR = 1.20, 95% CI = 1.09-1.32), and rs9810566 at 3q26.2 near TNIK (Pcombined = 1...
February 28, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334807/allele-specific-quantitative-proteomics-unravels-molecular-mechanisms-modulated-by-cis-regulatory-pparg-locus-variation
#14
Heekyoung Lee, Kun Qian, Christine von Toerne, Lena Hoerburger, Melina Claussnitzer, Christoph Hoffmann, Viktoria Glunk, Simone Wahl, Michaela Breier, Franziska Eck, Leili Jafari, Sophie Molnos, Harald Grallert, Ingrid Dahlman, Peter Arner, Cornelia Brunner, Hans Hauner, Stefanie M Hauck, Helmut Laumen
Genome-wide association studies identified numerous disease risk loci. Delineating molecular mechanisms influenced by cis-regulatory variants is essential to understand gene regulation and ultimately disease pathophysiology. Combining bioinformatics and public domain chromatin information with quantitative proteomics supports prediction of cis-regulatory variants and enabled identification of allele-dependent binding of both, transcription factors and coregulators at the type 2 diabetes associated PPARG locus...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334792/gwas-identifies-population-specific-new-regulatory-variants-in-fut6-associated-with-plasma-b12-concentrations-in-indians
#15
Suraj S Nongmaithem, Charudatta V Joglekar, Ghattu V Krishnaveni, Sirazul A Sahariah, Meraj Ahmad, Swetha Ramachandran, Meera Gandhi, Harsha Chopra, Anand Pandit, Ramesh D Potdar, Caroline Hd Fall, Chittaranjan S Yajnik, Giriraj R Chandak
Vitamin B12 is an important cofactor in one-carbon metabolism whose dysregulation is associated with various clinical conditions. Indians have a high prevalence of B12 deficiency but little is known about the genetic determinants of circulating B12 concentrations in Indians. We performed a genome-wide association study in 1001 healthy participants in the Pune Maternal Nutrition Study (PMNS), replication studies in 3418 individuals from other Indian cohorts and by meta-analysis identified new variants, rs3760775 (p = 1...
February 27, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334615/the-ncam1-gene-set-is-linked-to-depressive-symptoms-and-their-brain-structural-correlates-in-healthy-individuals
#16
Jana Petrovska, David Coynel, Matthias Fastenrath, Annette Milnik, Bianca Auschra, Tobias Egli, Leo Gschwind, Francina Hartmann, Eva Loos, Klara Sifalakis, Christian Vogler, Dominique J-F de Quervain, Andreas Papassotiropoulos, Angela Heck
Depressive symptoms exist on a continuum, the far end of which is found in depressive disorders. Utilizing the continuous spectrum of depressive symptoms may therefore contribute to the understanding of the biological underpinnings of depression. Gene set enrichment analysis (GSEA) is an important tool for the identification of gene groups linked to complex traits, and was applied in the present study on genome-wide association study (GWAS) data of depression scores and their brain-level structural correlates in healthy young individuals...
March 6, 2017: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/28334354/methodological-implementation-of-mixed-linear-models-in-multi-locus-genome-wide-association-studies
#17
Yang-Jun Wen, Hanwen Zhang, Yuan-Li Ni, Bo Huang, Jin Zhang, Jian-Ying Feng, Shi-Bo Wang, Jim M Dunwell, Yuan-Ming Zhang, Rongling Wu
No abstract text is available yet for this article.
March 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334342/tagging-snp-set-selection-with-maximum-information-based-on-linkage-disequilibrium-structure-in-genome-wide-association-studies
#18
Shudong Wang, Sicheng He, Fayou Yuan, Xinjie Zhu
Motivation: Effective tagging single-nucleotide polymorphism (SNP)-set selection is crucial to SNP-set analysis in genome-wide association studies (GWAS). Most of the existing tagging SNP-set selection methods cannot make full use of the information hidden in common or rare variants associated diseases. It is noticed that some SNPs have overlapping genetic information owing to linkage disequilibrium (LD) structure between SNPs. Therefore, when testing the association between SNPs and disease susceptibility, it is sufficient to elect the representative SNPs (called tag SNP-set or tagSNP-set) with maximum information...
March 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334340/meta-analytic-framework-for-liquid-association
#19
Lin Wang, Silvia Liu, Ying Ding, Shin-Sheng Yuan, Yen-Yi Ho, George C Tseng
Motivation: Although coexpression analysis via pair-wise expression correlation is popularly used to elucidate gene-gene interactions at the whole-genome scale, many complicated multi-gene regulations require more advanced detection methods. Liquid association is a powerful tool to detect the dynamic correlation of two gene variables depending on the expression level of a third variable (LA scouting gene). Liquid association detection from single transcriptomic study, however, is often unstable and not generalizable due to cohort bias, biological variation, and limited sample size...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334273/gwas-summary-based-pathway-analysis-correcting-for-the-genetic-confounding-impact-of-environmental-exposures
#20
Qianrui Fan, Feng Zhang, Wenyu Wang, Jiawen Xu, Jingcan Hao, Awen He, Yan Wen, Ping Li, Xiao Liang, Yanan Du, Li Liu, Cuiyan Wu, Sen Wang, Xi Wang, Yujie Ning, Xiong Guo
Genome-wide association study (GWAS)-based pathway association analysis is a powerful approach for the genetic studies of human complex diseases. However, the genetic confounding effects of environment exposure-related genes can decrease the accuracy of GWAS-based pathway association analysis of target diseases. In this study, we developed a pathway association analysis approach, named Mendelian randomization-based pathway enrichment analysis (MRPEA), which was capable of correcting the genetic confounding effects of environmental exposures, using the GWAS summary data of environmental exposures...
March 8, 2017: Briefings in Bioinformatics
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